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GUNC: detection of chimerism and contamination in prokaryotic genomes
Open accessAbstract
Genomes are critical units in microbiology, yet ascertaining quality in prokaryotic genome assemblies remains a formidable challenge. We present GUNC (the Genome UNClutterer), a tool that accurately detects and quantifies genome chimerism based on the lineage homogeneity of individual contigs using a genome’s full complement of genes. GUNC complements existing approaches by targeting previously underdetected types of contamination: we conservatively estimate that 5.7% of genomes in GenBank, 5.2% in RefSeq, and 15–30% of pre-filtered “high-quality” metagenome-assembled genomes in recent studies are undetected chimeras. GUNC provides a fast and robust tool to substantially improve prokaryotic genome quality.
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Cites
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Cited by
Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkab776 · Cited by 2,402
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Rapid and sensitive detection of genome contamination at scale with FCS-GX
Astashyn, A., Tvedte, E. S., Sweeney, D., Sapojnikov, V., Bouk, N., Joukov, V., Mozes, E., Strope, P. K., Sylla, P. M., Wagner, L., et al. (2024) · Genome Biology · doi:10.1186/s13059-024-03198-7 · Cited by 469
Drivers and determinants of strain dynamics following fecal microbiota transplantation
Schmidt, T. S. B., Li, S. S., Maistrenko, O. M., Akanni, W., Coelho, L. P., Dolai, S., Fullam, A., Glazek, A. M., Hercog, R., Herrema, H., et al. (2022) · Nature Medicine · doi:10.1038/s41591-022-01913-0 · Cited by 233
Self-citationBeresford-Jones, B. S., Forster, S. C., Stares, M. D., Notley, G., Viciani, E., Browne, H. P., Boehmler, D. J., Soderholm, A. T., Kumar, N., Vervier, K., et al. (2022) · Cell Host & Microbe · doi:10.1016/j.chom.2021.12.003 · Cited by 194
Metadata
- Authors
- Orakov, A., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B., & Bork, P.
- Venue
- Genome Biology
- Published
- 2021-06-13
- Volume
- 22
- Issue
- 1
- Pages
- 178-178
- ISSN
- 1465-6906 (ISSN-L)
- 1474-760X
- OpenAlex
- W3168040031
- Cited by
- 299
- References
- 50
- FWCI
- 11.61
- Type
- journal article
- Language
- en
- Open access
- gold
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- Orakov, A., Fullam, A., Coelho, L. P., Khedkar, S., Szklarczyk, D., Mende, D. R., Schmidt, T. S. B., & Bork, P. (2021). GUNC: detection of chimerism and contamination in prokaryotic genomes. Genome Biology. https://doi.org/10.1186/s13059-021-02393-0
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